Assessment of geographical accessibility to COVID-19 testing facilities in Nepal (2021).

Background: Ensuring equitable physical access to SARS-CoV-2 testing has proven to be crucial for controlling the COVID-19 epidemic, especially in countries like Nepal with its challenging terrain. During the second wave of the pandemic in May 2021, there was immense pressure to expand the laboratory network in Nepal to ensure calibration of epidemic response. The expansion led to an increase in the number of testing facilities from 69 laboratories in May 2021 to 89 laboratories by November 2021. We assessed the equity of physical access to COVID-19 testing facilities in Nepal during 2021. Furthermore, we investigated the potential of mathematical optimisation in improving accessibility to COVID-19 testing facilities. Methods: Based on up-to-date publicly available data sets and on the COVID-19-related daily reports published by Nepal's Ministry of Health and Population from May 1 to November 15, 2021, we measured the disparities in geographical accessibility to COVID-19 testing across Nepal at a resolution of 1 km2. In addition, we proposed an optimisation model to prescribe the best possible locations to set up testing laboratories maximizing access, and tested its potential impact in Nepal. Findings: The analysis identified vulnerable districts where, despite ramping up efforts, physical accessibility to testing facilities remains low under two modes of travel-walking and motorized driving. Both geographical accessibility and its equality were better under the motorised mode compared with the walking mode. If motorised transportation were available to everyone, the population coverage within 60 min of any testing facility (public and private) would be close to threefold the coverage for pedestrians within the same hour: 61.4% motorised against 22.2% pedestrian access within the hour, considering the whole population of Nepal. Very low accessibility was found in most areas except those with private test centres concentrated in the capital city of Kathmandu. The hypothetical use of mathematical optimisation to select 20 laboratories to add to the original 69 could have improved access from the observed 61.4% offered by the laboratories operating in November to 71.4%, if those 20 could be chosen optimally from all existing healthcare facilities in Nepal. In mountainous terrain, accessibility is very low and could not be improved, even considering all existing healthcare facilities as potential testing locations. Interpretation: The findings related to geographical accessibility to COVID-19 testing facilities should provide valuable information for health-related planning in Nepal, especially in emergencies where data might be limited and decisions time-sensitive. The potential use of publicly available data and mathematical optimisation could be considered in the future. Funding: WHO Special Programme for Research and Training in Tropical Diseases (TDR).

Health Emergency Risk Management in World Health Organization - South-East Asia Region during 2014-2023: synthesis of experiences.

Health Emergency Risk Management (ERM) has become increasingly critical on the global stage, prompted by the escalating frequency and severity of natural disasters and disease outbreaks. This paper offers a comprehensive synthesis of the World Health Organization's (WHO) experiences in the South-East Asia Region during the period 2014-2023, shedding light on its efforts to manage health emergencies and enhance resilience. The South-East Asia Region's unique environmental and economic diversity exposes it to significant health risks, including emerging infectious diseases and their implications for development, particularly in low-income countries. Here we document the transition from reactive emergency responses to proactive preparedness, catalyzed by prioritizing ERM as one of the regional flagship priorities in 2014. Key components of this initiative included capacity-building, the establishment of the South-East Asia Regional Health Emergency Fund (SEARHEF), and the implementation of the International Health Regulations (IHR 2005). This synthesis highlights the region's achievements in event reporting, development of national actions plan, successful Early Warning, Alert, and Response System (EWARS) implementation, and improvements in core capacities under IHR (2005). It also underscores the challenges associated with cross-border data sharing and regional collaboration that could strengthen ERM and enhance readiness for effective synergistic response.

Strengthening pathogen genomic surveillance for health emergencies: insights from the World Health Organization's regional initiatives.

The onset of the COVID-19 pandemic triggered a rapid scale-up in the use of genomic surveillance as a pandemic preparedness and response tool. As a result, the number of countries with in-country SARS-CoV-2 genomic sequencing capability increased by 40% from February 2021 to July 2022. The Global Genomic Surveillance Strategy for Pathogens with Pandemic and Epidemic Potential 2022-2032 was launched by the World Health Organization (WHO) in March 2022 to bring greater coherence to ongoing work to strengthen genomic surveillance. This paper describes how WHO's tailored regional approaches contribute to expanding and further institutionalizing the use of genomic surveillance to guide pandemic preparedness and response measures as part of a harmonized global undertaking. Challenges to achieving this vision include difficulties obtaining sequencing equipment and supplies, shortages of skilled staff, and obstacles to maximizing the utility of genomic data to inform risk assessment and public health action. WHO is helping to overcome these challenges in collaboration with partners. Through its global headquarters, six regional offices, and 153 country offices, WHO is providing support for country-driven efforts to strengthen genomic surveillance in its 194 Member States, with activities reflecting regional specificities. WHO's regional offices serve as platforms for those countries in their respective regions to share resources and knowledge, engage stakeholders in ways that reflect national and regional priorities, and develop regionally aligned approaches to implementing and sustaining genomic surveillance within public health systems.

Global disparities in SARS-CoV-2 genomic surveillance.

Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time <21 days, could provide a benchmark for SARS-CoV-2 genomic surveillance. Socioeconomic inequalities undermine the global pandemic preparedness, and efforts must be made to support low- and middle-income countries improve their local sequencing capacity.

Melioidosis in Africa: Time to Raise Awareness and Build Capacity for Its Detection, Diagnosis, and Treatment.

Melioidosis is a tropical infectious disease caused by the soil-dwelling bacterium Burkholderia pseudomallei with a mortality of up to 50% in low resource settings. Only a few cases have been reported from African countries. However, studies on the global burden of melioidosis showed that Africa holds a significant unrecognized disease burden, with Nigeria being at the top of the list. The first World Health Organization African Melioidosis Workshop was organized in Lagos, Nigeria, with representatives of health authorities, microbiology laboratories, and clinical centers from across the continent. Dedicated hands-on training was given on laboratory diagnostics of B. pseudomallei. This report summarises the meeting objectives, including raising awareness of melioidosis and building capacity for the detection, diagnosis, biosafety, treatment, and prevention across Africa. Further, collaboration with regional and international experts provided a platform for sharing ideas on best practices.

Exportation of Monkeypox Virus From the African Continent.

BACKGROUND: The largest West African monkeypox outbreak began September 2017, in Nigeria. Four individuals traveling from Nigeria to the United Kingdom (n = 2), Israel (n = 1), and Singapore (n = 1) became the first human monkeypox cases exported from Africa, and a related nosocomial transmission event in the United Kingdom became the first confirmed human-to-human monkeypox transmission event outside of Africa. METHODS: Epidemiological and molecular data for exported and Nigerian cases were analyzed jointly to better understand the exportations in the temporal and geographic context of the outbreak. RESULTS: Isolates from all travelers and a Bayelsa case shared a most recent common ancestor and traveled to Bayelsa, Delta, or Rivers states. Genetic variation for this cluster was lower than would be expected from a random sampling of genomes from this outbreak, but data did not support direct links between travelers. CONCLUSIONS: Monophyly of exportation cases and the Bayelsa sample, along with the intermediate levels of genetic variation, suggest a small pool of related isolates is the likely source for the exported infections. This may be the result of the level of genetic variation present in monkeypox isolates circulating within the contiguous region of Bayelsa, Delta, and Rivers states, or another more restricted, yet unidentified source pool.

Global disparities in SARS-CoV-2 genomic surveillance.

Genomic sequencing provides critical information to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments and vaccines, and guide public health responses. To investigate the spatiotemporal heterogeneity in the global SARS-CoV-2 genomic surveillance, we estimated the impact of sequencing intensity and turnaround times (TAT) on variant detection in 167 countries. Most countries submit genomes >21 days after sample collection, and 77% of low and middle income countries sequenced <0.5% of their cases. We found that sequencing at least 0.5% of the cases, with a TAT <21 days, could be a benchmark for SARS-CoV-2 genomic surveillance efforts. Socioeconomic inequalities substantially impact our ability to quickly detect SARS-CoV-2 variants, and undermine the global pandemic preparedness.

Regional sequencing collaboration reveals persistence of the T12 Vibrio cholerae O1 lineage in West Africa.

Background: Despite recent insights into cholera transmission patterns in Africa, regional and local dynamics in West Africa-where cholera outbreaks occur every few years-are still poorly understood. Coordinated genomic surveillance of Vibrio cholerae in the areas most affected may reveal transmission patterns important for cholera control. Methods: During a regional sequencing workshop in Nigeria, we sequenced 46 recent V. cholerae isolates from Cameroon, Niger, and Nigeria (37 from 2018 to 2019) to better understand the relationship between the V. cholerae bacterium circulating in these three countries. Results: From these isolates, we generated 44 whole Vibrio cholerae O1 sequences and analyzed them in the context of 1280 published V. cholerae O1 genomes. All sequences belonged to the T12 V. cholerae seventh pandemic lineage. Conclusions: Phylogenetic analysis of newly generated and previously published V. cholerae genomes suggested that the T12 lineage has been continuously transmitted within West Africa since it was first observed in the region in 2009, despite lack of reported cholera in the intervening years. The results from this regional sequencing effort provide a model for future regionally coordinated surveillance efforts. Funding: Funding for this project was provided by Bill and Melinda Gates Foundation OPP1195157.

PIPDeploy: Development and implementation of a gamified table top simulation exercise to strengthen national pandemic vaccine preparedness and readiness.

Successful emergency vaccination campaigns rely on effective deployment and vaccination plans. This applies to localised outbreaks as well as for pandemics. In the wake of the 2009 H1N1 influenza pandemic, analysis of the global Vaccine Deployment Initiative, through which the World Health Organization (WHO) donated pandemic influenza vaccines to countries in need, revealed that an absence of vaccine deployment plans in many countries significantly hindered vaccine deployment. Through the Pandemic Influenza Preparedness Framework adopted by the World Health Assembly in 2011, WHO is engaging in several capacity building activities to improve pandemic influenza preparedness and response and make provisions for access to vaccines and sharing of other benefits. The Framework calls for the development and exercise of operational plans for deployment of influenza vaccines to enhance pandemic preparedness. To this end, WHO has supported the development of PIPDeploy, an interactive, in-person table top simulation exercise to facilitate learning for emergency preparedness. It employs various game design elements including a game board, time pressure, leaderboards and teams to enhance participants' motivation. PIPDeploy formed part of five WHO Pandemic Influenza Vaccine Deployment Workshops attended by national-level managers responsible for pandemic influenza vaccine response predominantly in non-producing countries. The purpose of this study was to describe the features and application of PIPDeploy, and present findings of the evaluation of participants' experiences during the simulation involving a "hot wash" discussion and collection of quantitative data. The simulation's instructional approach was widely accepted by participants, who reported that the format was novel and engaging. They reflected on its utility for identifying gaps in their own vaccine deployment plans and regulatory frameworks for importation of vaccine products. All participants found the simulation relevant to their professional objectives. A range of other potential applications were suggested, including PIPDeploy's adaptation to sub-national contexts and to other epidemic diseases.

Design thinking during a health emergency: building a national data collection and reporting system.

BACKGROUND: Design thinking allows challenging problems to be redefined in order to identify alternative user-center strategies and solutions. To address the many challenges associated with collecting and reporting data during the 2014 Ebola outbreak in Guinea, Liberia and Sierra Leone, we used a design thinking approach to build the Global Ebola Laboratory Data collection and reporting system. MAIN TEXT: We used the five-stage Design Thinking model proposed by Hasso-Plattner Institute of Design at Stanford in Guinea, Liberia and Sierra Leone. This approach offers a flexible model which focuses on empathizing, defining, ideating, prototyping, and testing. A strong focus of the methodology includes end-users' feedback from the beginning to the end of the process. This is an iterative methodology that continues to adapt according to the needs of the system. The stages do not need to be sequential and can be run in parallel, out of order, and repeated as necessary. Design thinking was used to develop a data collection and reporting system, which contains all laboratory data from the three countries during one of the most complicated multi-country outbreaks to date. The data collection and reporting system was used to orient the response interventions at the district, national, and international levels within the three countries including generating situation reports, monitoring the epidemiological and operational situations, providing forecasts of the epidemic, and supporting Ebola-related research and the Ebola National Survivors programs within each country. CONCLUSIONS: Our study demonstrates the numerous benefits that arise when using a design thinking methodology during an outbreak to solve acute challenges within the national health information system and the authors recommend it's use during future complex outbreaks.

Systems thinking for health emergencies: use of process mapping during outbreak response.

Process mapping is a systems thinking approach used to understand, analyse and optimise processes within complex systems. We aim to demonstrate how this methodology can be applied during disease outbreaks to strengthen response and health systems. Process mapping exercises were conducted during three unique emerging disease outbreak contexts with different: mode of transmission, size, and health system infrastructure. System functioning improved considerably in each country. In Sierra Leone, laboratory testing was accelerated from 6 days to within 24 hours. In the Democratic Republic of Congo, time to suspected case notification reduced from 7 to 3 days. In Nigeria, key data reached the national level in 48 hours instead of 5 days. Our research shows that despite the chaos and complexities associated with emerging pathogen outbreaks, the implementation of a process mapping exercise can address immediate response priorities while simultaneously strengthening components of a health system.

Enhancing laboratory capacity during Ebola virus disease (EVD) heightened surveillance in Liberia: lessons learned and recommendations.

INTRODUCTION: Following a declaration by the World Health Organization that Liberia had successfully interrupted Ebola virus transmission on May 9th, 2015; the country entered a period of enhanced surveillance. The number of cases had significantly reduced prior to the declaration, leading to closure of eight out of eleven Ebola testing laboratories. Enhanced surveillance led to an abrupt increase in demand for laboratory services. We report interventions, achievements, lessons learned and recommendations drawn from enhancing laboratory capacity. METHODS: Using archived data, we reported before and after interventions that aimed at increasing laboratory capacity. Laboratory capacity was defined by number of laboratories with Ebola Virus Disease (EVD) testing capacity, number of competent staff, number of specimens tested, specimen backlog, daily and surge testing capacity, and turnaround time. Using Stata 14 (Stata Corporation, College Station, TX, USA), medians and trends were reported for all continuous variables. RESULTS: Between May and December 2015, interventions including recruitment and training of eight staff, establishment of one EVD laboratory facility, implementation of ten Ebola GeneXpert diagnostic platforms, and establishment of working shifts yielded an 8-fold increase in number of specimens tested, a reduction in specimens backlog to zero, and restoration of turn-around time to 24 hours. This enabled a more efficient surveillance system that facilitated timely detection and containment of two EVD clusters observed thereafter. CONCLUSION: Effective enhancement of laboratory services during high demand periods requires a combination of context-specific interventions. Building and ensuring sustainability of local capacity is an integral part of effective surveillance and disease outbreak response efforts.

Measures to control protracted large Lassa fever outbreak in Nigeria, 1 January to 28 April 2019.

Lassa fever cases have increased in Nigeria since 2016 with the highest number, 633 cases, reported in 2018. From 1 January to 28 April 2019, 554 laboratory-confirmed cases including 124 deaths were reported in 21 states in Nigeria. A public health emergency was declared on 22 January by the Nigeria Centre for Disease Control. We describe the various outbreak responses that have been implemented, including establishment of emergency thresholds and guidelines for case management.

Complete Genome Sequence of a Hepatitis E Virus Genotype 1e Strain from an Outbreak in Nigeria, 2017.

Hepatitis E virus genotype 1 (HEV-1) is associated with large epidemics. Notably, HEV subtype 1e (HEV-1e) has caused HEV outbreaks in sub-Saharan Africa. We report here the second full-length genome sequence of an HEV-1e strain (NG/17-0503) from a recent outbreak in Nigeria in 2017. It shares 94.2% identity with an HEV-1e strain from Chad.

A new hepatitis E virus genotype 2 strain identified from an outbreak in Nigeria, 2017.

BACKGROUND: In 2017 the Nigerian Ministry of Health notified the World Health Organization (WHO) of an outbreak of hepatitis E located in the north-east region of the country with 146 cases with 2 deaths. The analysis of the hepatitis E virus (HEV) genotypes responsible for the outbreak revealed the predominance of HEV genotypes 1 (HEV-1) and 2 (HEV-2). Molecular data of HEV-2 genomes are limited; therefore we characterized a HEV-2 strain of the outbreak in more detail. FINDING: The full-length genome sequence of an HEV-2 strain (NG/17-0500) from the outbreak was amplified using newly designed consensus primers. Comparison with other HEV complete genome sequences, including the only HEV-2 strain (Mex-14) with available complete genome sequences and the availability of data of partial HEV-2 sequences from Sub-Saharan Africa, suggests that NG/17-0500 belongs to HEV subtype 2b (HEV-2b). CONCLUSIONS: We identified a novel HEV-2b strain from Sub-Saharan Africa, which is the second complete HEV-2 sequence to date, whose natural history and epidemiology merit further investigation.

Outbreak of Neisseria meningitidis serogroup C outside the meningitis belt-Liberia, 2017: an epidemiological and laboratory investigation.

BACKGROUND: On April 25, 2017, a cluster of unexplained illnesses and deaths associated with a funeral was reported in Sinoe County, Liberia. Molecular testing identified Neisseria meningitidis serogroup C (NmC) in specimens from patients. We describe the epidemiological investigation of this cluster and metagenomic characterisation of the outbreak strain. METHODS: We collected epidemiological data from the field investigation and medical records review. Confirmed, probable, and suspected cases were defined on the basis of molecular testing and signs or symptoms of meningococcal disease. Metagenomic sequences from patient specimens were compared with 141 meningococcal isolate genomes to determine strain lineage. FINDINGS: 28 meningococcal disease cases were identified, with dates of symptom onset from April 21 to April 30, 2017: 13 confirmed, three probable, and 12 suspected. 13 patients died. Six (21%) patients reported fever and 23 (82%) reported gastrointestinal symptoms. The attack rate for confirmed and probable cases among funeral attendees was 10%. Metagenomic sequences from six patient specimens were similar to a sequence type (ST) 10217 (clonal complex [CC] 10217) isolate genome from Niger, 2015. Multilocus sequencing identified five of seven alleles from one specimen that matched ST-9367, which is represented in the PubMLST database by one carriage isolate from Burkina Faso, in 2011, and belongs to CC10217. INTERPRETATION: This outbreak featured high attack and case fatality rates. Clinical presentation was broadly consistent with previous meningococcal disease outbreaks, but predominance of gastrointestinal symptoms was unusual compared with previous African meningitis epidemics. The outbreak strain was genetically similar to NmC CC10217, which caused meningococcal disease outbreaks in Niger and Nigeria. CC10217 had previously been identified only in the African meningitis belt. FUNDING: US Global Health Security.